Browsing by Subject "Evolution"
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Item Adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung environment(2013-12) Huse, Holly Kristen; Whiteley, MarvinChronic microbial infections result from persistent host colonization that is not cleared via the immune response or therapeutics. Within the host, microbes can undergo adaptive evolution, whereby beneficial traits promoting persistence arise due to selection; these traits can therefore affect disease outcomes and treatment strategies. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa is the primary cause of chronic, fatal respiratory infections in individuals with the heritable disease cystic fibrosis (CF). The goal of this dissertation is to identify adaptations that allow P. aeruginosa to persist in the host during chronic CF lung infection. To achieve this goal, P. aeruginosa was chronologically sampled from 3 CF patients, ranging from the first infecting bacterium (the ancestor) to ~40,000 generations post-infection. By comparing gene expression profiles of ancestral and evolved isolates sampled from multiple patients, I identified 24 parallel gene expression changes that occurred over time within each lineage, suggesting that these traits are beneficial to the bacterium. Because most of these traits had unknown physiological roles, I sought to characterize their biological significance. I used a gain-of-function genetic screen and discovered that a subset of these genes enhance biofilm formation, a sessile mode of growth proposed to be important during chronic CF lung infection. I showed that enhanced biofilm formation is due to increased production of the exopolysaccharide Psl, which is traditionally viewed as less critical for maintaining chronic infections than other virulence factors. Lastly, I demonstrated that a majority (~72%) of chronic P. aeruginosa isolates produce more Psl than their corresponding ancestor, suggesting that this exopolysaccharide is important during chronic infection and an adaptive trait.Item Analysis of factors influencing the teaching of evolution and creationism in Texas public high school biology classes(Texas Tech University, 1989-12) Shankar, GangaThis research examined the emphasis given by Texas high school biology teachers to evolution and creationism. Selected variables were analyzed to determine their influence on the teaching of evolution and creationism. Data were obtained through a questionnaire administered by mail to a random sample of Texas public high school biology teachers during spring, 1988. Results obtained from 307 teachers, who represented 50 percent of the sample receiving the questionnaire, indicated that the majority of Texas biology teachers taught evolution, but did not give it comprehensive coverage as indicated by total time allocated to evolution and twelve topics concerned with evolution. The majority of the teachers thought evolution should be taught in high school biology because of its role as a unifying and central theme in biology.Item Assessing conserved function of conidiation regulators in two distantly related ascomycetes, Aspergillus nidulans and Neurospora crassa(2012-07-16) Chung, Da WoonConidiation is a common and critical asexual reproductive mode in fungi. The ascomycetes, the largest group in the kingdom Fungi undergo conidiation. The wide array of morphological difference in a conidiophore and conidial size, shape, and cellular organization demonstrates the importance of evolution in driving the morphological and functional diversity. An important unanswered question is how these conidiation processes evolve. We hypothesized that a conidiation regulatory pathway was present in the ancestral species, and became specialized in the extant species to lead to morphological and functional diversity. To address this hypothesis we assessed the conserved function of conidiation regulators in two distantly related ascomycetes, Aspergillus nidulans and Neurospora crassa. Using sequence similarity analysis, N. crassa orthologs were characterized to seven main conidiation regulatory genes in A. nidulans (fluG, flbC, flbD, abaA, wetA, medA, and stuA). Expression of the N. crassa orthologs complemented defective conidiation in the A. nidulans fluG, flbD, wetA, medA, and stuA mutants. In contrast, abaA and flbC and the N. crassa orthologs did not share conserved biochemical function. Taken in context of other recent studies of conidiation regulators, there are four distinct evolutionary patterns: (i) Non-homologous genes with analogous roles in conidiation (?brlA? and ?fl?), (ii) Orthologs with retained biochemical function that lack analogous role in conidiation (?fluG?, ?flbD?, and ?wetA?), (iii) Orthologs with retained biochemical function and analogous roles in conidiation (?medA? and ?stuA?), and (iv) Orthologs with biochemical function not conserved but with analogous roles in conidiation (?abaA? and ?flbC?). These studies set the stage for long-term studies of how evolution proceeded during the evolution of conidiation at different levels of phylogenetic diversity. An understanding of how evolutionary mechanisms shape the dynamics of developmental pathways will be significant for our understanding of fungal evolution of other novel adaptations such as pathogenesis.Item Characterization of beneficial mutations in unsaturated fatty acid biosynthesis that are recurrent dead-ends in a long-term evolution experiment with Escherichia coli(2014-05) Wolf, Lindsey Nan; Barrick, Jeffrey E.; Bull, JamesMicrobes provide an invaluable tool for watching evolution in action. Throughout more than 55,000 generations, lineages of Escherichia coli cells in a long-term evolution experiment (LTEE) grew in a minimal glucose environment and explored different mutational paths to higher fitness. Genome sequencing identifies genes that accrue mutations early in evolution across the twelve evolving populations. These parallel mutations typically provide a significant fitness benefit and often fix in the population. However, some mutations seem to lead to evolutionary dead-ends. In 7 of the 12 LTEE populations, lineages with mutations in the gene coding for the lipid synthesis repressor, fabR, gain traction within the population, but always eventually go extinct. To parse out the fitness benefits and downstream effects, strains with these mutations were constructed. These mutations increase the growth rate and may affect the length of lag phase after each daily transfer. Another mutation that often fixes within eventually successful clades is within the stress response global regulator spoT. A connection between spoT and fabR mutations could be the key to understanding the eventual outcomes within these lineages. Decreased fatty acid synthesis (repressed by FabR) during glucose starvation activates the global repressor SpoT to produce the cellular "alarmone" (p)ppGpp, inhibiting cell growth during the stringent response. Thus, it is possible that fabR mutations that prolong fatty acid synthesis and spoT mutations that alter the production of (p)ppGpp may both benefit cells by affecting the stringent response. In addition, when these two mutations are combined in a single strain they confer nearly an identical increase in fitness as the single mutations alone, strengthening the argument that they may target the same cellular pathway. Preliminary gene expression analyses of fabR mutants confirmed an expected increase in unsaturated fatty acid synthesis and also found signs that membrane damage responses were activated. It is possible that fabR mutants are near a stability cliff that makes them unable to access otherwise beneficial further mutations. Ultimately, this work will elucidate how interactions between the physiological effects of mutations on evolutionary paths to higher fitness may lead to differences in evolvability that ultimately determine success or extinction.Item The cognitive biology of mate choice in túngara frogs (Physalaemus pustulosus)(2010-05) Akre, Karin Lise; Ryan, Michael J. (Michael Joseph), 1953-; Cummings, Molly E.; Domjan, Michael; Fuiman, Lee A.; Mueller, Ulrich G.Sexual selection is responsible for a great diversity of elaborate male traits. A general female preference for males that have exaggerated traits drives this process, but the reasons females exhibit this preference are often unclear. Recent advances in understanding signal evolution have emerged from studies of receiver psychology that focus on how receivers perceive and process communication signals. I apply the perspective of receiver psychology to understand female preference for elaborate signals in túngara frogs (Physalaemus pustulosus). Male túngara frogs produce advertisement calls of variable complexity. Females exhibit a strong preference for complex to simple calls, but previous studies have not found consistent patterns of preference between calls of variable complexity. In my doctoral research, I investigate the function of variable complexity in túngara frogs. Specifically, I address the following questions: 1) Are calls of variable complexity especially relevant to females in certain contexts? Do males respond to female behavior by increasing their production of complex calls? 2) Does male to female proximity influence female response to call complexity? 3) Are females constrained by their perceptual biology in discriminating differences in call complexity? 4) Can females remember attractive males over silences between bouts of advertising? Is working memory for attractive males dependent upon signal complexity? And 5) Does signal memorability increase with signal complexity in a linear relationship? These studies provide several new perspectives to an understanding of female preference for elaborate signals. Phonotaxis experiments demonstrate that females use elicitation behaviors to influence male production of complex calls, that proximity influences female response to signal elaboration, that females are constrained by their perceptual biology in discriminating between complex calls, that memory can influence the evolution of signal complexity, and that memorability and signal complexity share a non-linear relationship.Item Complex eye formation in the squid Doryteuthis pealeii and its evolutionary implications(2015-12) Koenig, Kristen Marie; Gross, Jeffrey Martin; Marcotte, Edward M.; Juenger, Thomas; Zakon, Harold; Stein, DavidPhotoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. While the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the “eye” gene regulatory network remains controversial with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod, Doryteuthis pealeii, as a Lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays we characterize eye formation in Doryteuthis pealeii. Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris. Functional assays demonstrate that Notch signaling is required for photoreceptor cell formation and retina organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of conserved or convergent mechanisms.Item Convergent Evolution in Livebearing Fishes(2012-07-16) Troendle, NicholasThe directionality and consistency of evolution has long been a subject of contention among evolutionary biologists since the days of Darwin. However, it is unknown how much can be quantified and how much results from more complex variables. It is also unknown whether evolution is consistent or whether it occurs differently in each system. My study focuses on predation and habitat as ecological gradients that may create convergent evolution in livebearing fishes. In Chapter I, I focus on predation as a mechanism for driving convergent evolution in Gambusia affinis. A suite of 7 microsatellite markers was used in order to determine independence of morphological evolution. Mantel tests were used to compare genetic, phenotypic, geographical and environmental distances among the six focal populations. These tests showed that there was a significant correlation between genetic and geographic distance but no significant correlation between genetic and phenotypic distances, which may indicate that phenotypic divergence has arisen independently in multiple instances. The second chapter focuses on a unique form of convergence that arose during speciation of three livebearing fishes, which we termed "convergent speciation." I focus on habitat type as a selective pressure in the lake system of Lake Catemaco, Mexico and the surrounding rivers. Lake Catemaco has been isolated from the surrounding rivers for approximately 1.2 million years and during that time several endemic species have evolved in the lake. This provides an excellent study system for studying convergent divergence. To test the theory of convergent speciation in this system, a MANOVA was conducted. The effect of habitat was an important source of variance in the system, indicating that habitat is a likely driving force responsible for convergent speciation in the system. Using discriminant functions I was able to correctly predict the habitat of fish of six different species between 68% and 71% of the time. This may indicate that evolutionary response to habitat is consistent across taxa (i.e., convergent divergence is taking place).Item Developing hypotheses : evolutions in the poetics of Whitman and Melville(2013-05) McGinnis, Eileen Mary; Kevorkian, Martin, 1968-In the foundational scholarship on literature and evolution, there remains a tendency to focus on Darwinian evolution's influence on Victorian literature. Without ignoring Darwin's importance to both the late-19th century and our own time, this dissertation contributes to an emerging interest among historians and literary scholars in exploring the pre-Darwinian, transatlantic contexts of evolutionary discourse. By returning to a time when 'the development hypothesis' was a more fluid concept, we can examine how writers and poets on both sides of the Atlantic were able to actively shape its meanings and to use it as a framework for reflecting on their literary craft. In this dissertation, I argue that for Walt Whitman and Herman Melville, development is a key term in their particular constructions of a distinctive American literature in the 1840s and '50s. It underlies Whitman's conception of an experimental poetic voice in the 1855 Leaves of Grass as well as Melville's ambitions for literary narrative in Mardi and Moby-Dick. At the same time, the sweep of their careers well beyond the publication of Origin of Species in 1859---into the last decade of the nineteenth century---allows us to chart their later responses as evolution increasingly gained acceptance and Darwin became a front man of sorts for evolution. Although Whitman and Melville continue to incorporate evolution and scientific modernity into their late-career self-fashioning, we can trace a movement toward increasing distance, disillusionment, and abstraction in these deployments. This dissertation has implications not only for contemporary Whitman and Melville studies but also for re-assessing the broader trajectory of 19th-century American literary history. In conventional textbook accounts, the influence of Darwinian evolution is measured primarily in terms of the emergence of literary naturalism, a realist genre known for its unsparing look at lives caught in the scope of unsympathetic natural forces. Here, I suggest that developmental evolution offered alternative formal and epistemological possibilities for mid-19th-century American literature, enabling Whitman and Melville to develop hypotheses about literary truth and human value.Item Diversity and evolution of reproductive systems in Mycocepurus fungus-growing ants(2010-05) Rabeling, Christian; Mueller, Ulrich G.; Hillis, David M.; Bolnick, Daniel I.; Schultz, Theodore R.; Singer, Michael C.The general prevalence of sexual reproduction over asexual reproduction among metazoans testifies to the evolutionary, long-term benefits of genetic recombination. Despite the benefits of genetic recombination under sexual reproduction, asexual organisms sporadically occur throughout the tree of life, and a few asexual lineages persisted over significant evolutionary time without apparent recombination. The study of asexual organisms therefore may provide clues to answer why almost all eukaryotes reproduce via meiosis and syngamy and why asexual eukaryotes are almost always evolutionarily short-lived. Towards understanding the evolution of asexual lineages in the Hymenoptera, I first review the diversity of reproductive systems in the Hymenoptera, introduce the study organism, the fungus-gardening ant Mycocepurus smithii, and discuss my research objectives. Second, I integrate information from reproductive physiology, reproductive morphology, natural history and behavior, to document that that queens of M. smithii are capable of thelytokous parthenogenesis, workers are sterile, and males are absent from the surveyed population. These results suggest that M. smithii might be obligately asexual. To place the origin and maintenance of asexual reproduction in M. smithii in an evolutionary context, I use molecular phylogenetic and population-genetic methods to (i) test if M. smithii reproduces asexually throughout its distribution range; (ii) infer if asexuality evolved once or multiple times; (iii) date the origin of asexual reproduction in M. smithii; and (iv) elucidate the cytogenetic mechanism of thelytokous parthenogenesis. During field collecting for these studies throughout the Neotropics, I discovered a new species of obligate social parasite in the genus Mycocepurus. Social parasites are of great interest to evolutionary biology in order to elucidate mechanisms demonstrating how parasites gained reproductive isolation from their host species in sympatry. I describe this new parasite species, characterize its morphological and behavioral adaptations to the parasitic lifestyle, and discuss the parasite’s life history evolution in the context of social parasitism in fungus-growing ants. The dissertation research integrates population-genetic, phylogenetic, physiological and morphological approaches to advance our understanding of the evolution of reproductive systems and diversity of life-history traits in animals.Item The effects of a professional development program on elementary and middle school teachers’ understanding and acceptance of macroevolution and how they teach it(2013-12) Cid, Christina Ramsey; Petrosino, Anthony J. (Anthony Joseph), 1961-Despite science education reform efforts stressing the importance of understanding evolution, many students receive little to no exposure to the most important unifying concept in biology. Since evolution is basic to the study of biology, its study should begin with the introduction of the life sciences to students in elementary school. However, many teachers lack sufficient evolutionary content knowledge, have limited acceptance of evolution, and have little confidence to effectively teach it. Better teacher preparation is needed to meet the challenges of ensuring students develop conceptual understanding of evolution. While research shows the general public typically accepts microevolution while rejecting macroevolution, few studies have focused on peoples’ understanding of macroevolution. Additionally, little research exists examining the effects of an intervention on elementary and middle school teachers’ acceptance, understanding, and teaching of macroevolution. Using a conceptual framework based on the Cognitive Reconstruction of Knowledge Model, this study reports the effects of a sustained professional development program on 4th through 8th grade teachers’ acceptance of evolution; understanding of macroevolution; and approach to teaching evolution in schools, awareness of challenges to teaching evolution, and pedagogical content knowledge about teaching macroevolution. This study also explores the relationship between teachers’ understanding of macroevolution and acceptance of evolution. Various data sources, including the Measurement of the Understanding of Macroevolution (Nadelson & Southerland, 2010), the Measure of the Acceptance of the Theory of Evolution (Rutledge & Warden, 1999), teacher interviews, and teacher workshop reflections, were used to answer the research questions. Results from the study revealed that after attending the professional development series, teachers’ understanding of macroevolution and acceptance of evolution significantly increased. Acceptance of evolution was positively correlated to understanding of macroevolution. Teachers’ prior understanding of macroevolution was a significant positive predictor of their subsequent acceptance of evolution. Teachers’ prior acceptance of evolution was a significant predictor of their understanding of macroevolution, but only after teachers participated in at least half of the sustained professional development. Finally, teachers demonstrated having increased macroevolutionary pedagogical content knowledge. This effect was strong in those teachers who were initially low acceptors of evolution. The significance of these findings is discussed.Item Evolution in one of the world’s most abundant organisms, Prochlorococcus(2016-08) Olson, Todd James; Kirkpatrick, Mark, 1956-; Meyers, LaurenProchlorococcus is one of the most abundant organisms on the planet, and this abundance has the potential to give it unique evolutionary properties. Very large idealized populations experience very little drift. This relationship has caused many authors to assume that Prochlorococcus genomes have little to no drift, but care needs to be taken to understand how real populations of Prochlorococcus differ from idealized populations and how this affects their evolution. Part of this thesis is devoted to understanding a parameter called the effective population size, which is meant illustrate the amount of drift in real, non-idealized populations. Using our knowledge of effective population size we can then investigate the relative affects of selection and drift throughout the genome. We can use knowledge about which sites evolve primarily by selection to better understand interpretations of common genome statistics. Finally, I apply my findings about interpretations of genome statistics to literature on the evolution of Prochlorococcus genome size.Item The evolution of cooperation and conflict, experimental model systems and theory(2004) Sachs, Joel Lawrence; Bull, James J.I present three different studies in three chapters. In chapter 1, I describe a general theoretical framework for the evolution of cooperation both within and between species. Three general models are distinguished by which cooperation can evolve and be maintained: (i) directed reciprocation—cooperation with individuals who give in return; (ii) shared genes—cooperation with relatives; and (iii) byproduct benefits—cooperation as an incidental consequence of selfish action. In chapter 2, I investigate the origins of cooperation at the genotypic and phenotypic levels. While theory and empirical work enlighten the maintenance of cooperation, few studies explore its origins. Here, I examine the origins of cooperation by experimentally evolving two antagonistic bacteriophages. I experimentally enforced the two bacteriophages, f1 and IKe, to undergo fifty iterated cycles of co-infection, paired vertical transmission, and infectious transmission in Escherichia coli cells. Phenotypic and genomic analysis then characterized the outcome. Strikingly, the two bacteriophages evolved to co- package their genomes into one symbiotic unit, ensuring co-transmission during the infectious stage. Furthermore, one bacteriophage evolved a minimal genome with the inability to infect cells independently, becoming an obligate viral symbiont. These results parallel a wide variety of natural systems: evolution of reduced genomes, co-transmission of partners, and obligate coexistence between cooperating species. In chapter 3, I examine a puzzling example of cooperation between species, the symbiotic interaction that occurs in corals, hydras, and jellyfish and their dinoflagellate algae. These algae are mostly acquired infectiously, and according to models of virulence evolution should be selected to exploit the host. However, symbiont cheating is virtually unknown. I experimentally manipulated transmission mode of algal symbionts in jellyfish hosts to determine if altering symbiont transmission mode selects for cheating within symbiont populations. Cheating symbionts evolved under experimentally enforced horizontal transmission. Fitness estimates revealed that cheater algae had faster within-host growth, higher dispersal rates, and caused lower host growth compared to algae which underwent repeated vertical transmission. A trade-off was detected between harm caused to hosts and symbiont fitness. Such trade-offs have been modeled for pathogen evolution and may be critical in stabilizing ‘infectious’ symbioses.Item Evolution of Memory in Reactive Artificial Neural Networks(2012-07-16) Chung, Ji RyangIn the neuronal circuits of natural and artificial agents, memory is usually implemented with recurrent connections, since recurrence allows past agent state to affect the present, on-going behavior. Here, an interesting question arises in the context of evolution: how reactive agents could have evolved into cognitive ones with internalized memory? This study strives to find an answer to the question by simulating neuroevolution on artificial neural networks, with the hypothesis that internalization of external material interaction can be a plausible evolutionary path leading to a fully internalized memory system. A series of computational experiments were performed to gradually verify the above hypothesis. The first experiment demonstrated the possibility that external materials can be used as memory-aids for a memoryless reactive artificial agents in a simple 1-dimensional environment. Here, the reactive artificial agents used environmental markers as memory references to be successful in the ball-catching task that requires memory. Motivated by the result of the first experiment, an extended experiment was conducted to tackle a more complex memory problem using the same principle of external material interaction. This time, the reactive artificial agents are tasked to remember the locations of food items and the nest in a 2-dimensional environment. Such path-following behavior is a trivial foraging strategy of various lower animals such as ants and fish. The final experiment was designed to show the evolution of internal recurrence. In this experiment, I showed the evolutionary advantage of external material interaction by comparing the results from neural network topology evolution algorithms with and without the material interaction mechanism. The result confirmed that the agents with external material interaction learned to solve the memory task faster and more accurately. The results of the experiments provide insights on the possible evolutionary route to an internalized memory. The use of external material interaction can help reactive artificial agents to go beyond the functionality restricted by their simple network structure. Moreover, it allows much faster convergence with higher accuracy than the topological evolution of the artificial agents. These results suggest one plausible evolutionary path from reactive, through external material interaction, to recurrent structure.Item Evolution of microbial populations with spatial and environmental structure(2010-05) Miller, Eric Louis; Meyers, Lauren Ancel; Bennett, Philip C.; Bull, James J.; Hawkes, Christine V.; Hillis, David M.Rarely are natural conditions constant, but generally biologists study microbes in artificially constant environments in the laboratory. I relaxed these assumptions of constant environments through time and space as I investigated how microbial populations evolve. First, I examined how bacteriophage evolved in the presence of permissive and nonpermissive hosts. I found that bacteriophage evolved discrimina- tion in mixed environments as well as in one of two environments with homogeneous, permissive hosts. This showed the asymmetry of host-shifting in viruses as well as the possibility of large, and somewhat unpredictable, pleiotropic effects. Secondly, I reconstructed ancestral environmental conditions for soil bacteria groups using phy- logenetics and environmental variables of extant species’ habitats. These generaliza- tions suggested characteristic phenotypes for several phylogenetic groups, including uncultured Acidobacteria. Lastly, I collected genetic sequences and global collection information for 65 bacteria genera across the domain. In examining the relation- ship between genetic distance, environmental conditions, and geography, I observed positive relationships specifically between genetic distance and geography or genetic distance and environmental conditions for bacteria from land sites but not from wa- ter sites. Phylogenic classifications or phenotypes of the genera could not predict these correlations. In all of these projects, variations in the environment created evolutionary signals that hinted at past environments of microbial populations.Item The evolution of RNA and the actin protein family(2012-05) Keller, Thomas E.; Bull, James J.; Wilke, C. (Claus); Juenger, Thomas; Meyers, Lauren A; Sawyer, Sara LIn my dissertation I have broadly studied the evolution of RNA as well as the phylogenetic history of the actin protein family. In the first chapter I examined how various evolutionary processes interact at high mutation rates, which led to simple prediction based on the strength of selection. In the second chapter, I tested mRNA secondary structure stability at the beginning of genes as a way of identifying whether putative genes might be functional or not. Finally, I reconstructed the phylogenetic history of the actin protein family in vertebrates, revealing that a novel isoform is actively evolving in contrast to the remaining protein isoforms.Item Evolution, metabolism, and virulence of the oral microbiome(2013-12) Jorth, Peter Allan; Whiteley, MarvinThe human microbiome has important roles in maintaining health, but dysbiosis of the microbiota can lead to disease. Polymicrobial interactions can result in synergy, producing disease that is worse than the sum of the respective single species infections. Despite this significant impact, synergy is understudied due to the complexity of polymicrobial interactions. Periodontitis is a microbiome-associated disease, and is one of the most common infectious diseases worldwide. Therefore, we have used periodontal disease as a model to study polymicrobial synergy. I have used two complementary approaches to study polymicrobial infections. The opportunistic periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits synergy with streptococci in model murine infections. Because polymicrobial interactions are dependent on organisms’ abilities to sense their environments, I have examined the genetic regulatory mechanisms used by A. actinomycetemcomitans to interact with its environment. Through Northern blot analyses and biochemical approaches, I show that A. actinomycetemcomitans uses non-coding RNAs to regulate amino acid transport. Taking a comparative genomics approach, I demonstrate that A. actinomycetemcomitans DNA uptake systems are evolutionarily linked to genome defense. To describe host-influenced changes in gene expression, I develop a new technique to transcriptionally profile A. actinomycetemcomitans in a murine abscess infection, thereby revealing the importance of specific fermentative and anaerobic respiratory genes for in vivo survival. The long-term goal is to use these studies as a basis to characterize genetic regulatory mechanisms mediating synergy in polymicrobial A. actinomycetemcomitans infections with streptococci and other oral microbes. As a second approach to study polymicrobial infections, I analyze gene expression of healthy and diseased human plaque communities from aggressive periodontitis patients. Profiling ribosome content of healthy and diseased communities, I show that disease communities adopt similar less diverse population structures distinct from healthy populations. In addition to changes in population composition, using community transcriptional profiling I show that a keystone species within diseased communities up-regulates expression of genes involved in making the oral inflammatory molecule butyrate. These studies demonstrate for the first time that microbiome based diseases are marked by gene expression changes in addition to compositional changes.Item Evolutionary and ecological influences on color pattern variation in the Australian common froglet, Crinia signifera(2009-08) Symula, Rebecca E.; Cannatella, David C.; Hillis, David M., 1958-Elucidation of mechanisms that generate and maintain population-level phenotypic variability provides insight into processes that influence within-species genetic divergence. Historically, color pattern polymorphisms were used to infer population-level genetic variability, but recent approaches directly capture genetic variability using molecular markers. Here, I clarify the relationship between genetic variability and color pattern polymorphism within and among populations using the Australian common froglet, Crinia signifera. To illustrate genetic variability in C. signifera, I used phylogenetic analysis of mitochondrial DNA and uncovered three ancient geographically restricted lineages whose distributions are consistent with other southeastern Australian species. Additional phylogeographic structure was identified within the three ancient lineages and was consistent with geographic variation in male advertisement calls. Natural selection imposed by predators has been hypothesized to act on black-and-white ventral polymorphisms in C. signifera, specifically through mimicry of another Australian frog, Pseudophryne. I used clay replicas of C. signifera to test whether predators avoid black-and-white coloration. In fact, black-and-white replicas were preferentially avoided by predators in some habitats, but not in others, indicating that differential selection among habitats plays a role in maintaining color pattern polymorphism. When black-and-white color patterns in a sample of C. signifera populations were compared with those in sympatric Pseudophryne, several color pattern characteristics were correlated between the species. Furthermore, where C. signifera and Pseudophryne are sympatric, color patterns are more similar compared to those in allopatry. Extensive phylogenetic variability suggests that phylogenetic history and genetic drift may also influence C. signifera color pattern. Fine-scale phylogenetic analysis uncovered additional genetic diversity within lineages and low levels of introgression among previously identified clades. Measures of color pattern displayed low levels of phylogenetic signal, indicating that relationships among individuals only slightly influence color patterns. Finally, simulations of trait evolution under Brownian motion illustrated that the phylogeny alone cannot generate the pattern of variation observed in C. signifera color pattern. Therefore, this indicates a minimal role for genetic drift, but instead supports either the role of stabilizing selection due to mimicry, or diversifying selection due to habitat differences, in color pattern variation in C. signifera.Item Gene expression evolution after duplication(2015-12) Thompson, Ammon Michael; Zakon, H. H.; Hillis, David; Bull, James J; Gross, Jeff; Phelps, Steven MGene duplication is a mutational process that seeds genomes with new geneticmaterial. Ion channels comprise a large gene family that arose through gene duplicationsthat has played a substantial role in the evolution of novel traits across all of the domainsof life. For my dissertation, I investigated the evolutionary dynamics that allow geneduplicates to evolve novel functions. To do so, I focused on measuring and modeling theexpression evolution of voltage-gated sodium ion channel duplicates implicated in theconvergent evolution of electric organs in two families of electric fish.In chapter 1, I measured the expression stoichiometry of two sodium channelduplicates in electric fish species as well as non-electric relatives. I found that before amajor shift in expression from skeletal muscle and neofunctionalization in the musclederivedelectric organ, one of the duplicate genes was first down-regulated in theancestors of both electric lineages. In chapter 2, I introduce a new model of the dynamicsof duplicate genes co-evolving under dosage balance selection for their sharedexpression. I used the model to estimate the strength of selection on the duplicate genesfound in the electric fish lineages and to show that dosage balance selection impedes theevolution of novel function early after gene duplication but can later facilitate novelfunction evolution once a particular expression threshold is reached. In chapter 3 Iinvestigate the role a duplicate sodium channel played in the evolution of a novel electricorgan derived from motor neurons in a lineage of fish. In this lineage I show that aviskeletal-muscle-specific sodium channel duplicated and one of the duplicates gainedexpression in the spinal cord. In this tissue this channel exhibits sequence evolutionarypatterns consistent with it evolving to contribute to the unique electrophysiologicalattributes of the electric organ. This is the first observation of such a radical shift inexpression for a muscle-specific gene.Item Genes, judgments, and evolution : the social and political consequences of distributional and differential conflict(2012-05) Meyer, John Michael; Pedahzur, Ami; McDonald, PatrickThe following argument offers a sharper micro-foundational lens for studying human political and social behavior by demonstrating how political science might better incorporate the theory of evolution into its behavioral models, and by showing that differential conflict occasionally prevails over the materialist conflicts depicted in much of the modern social science literature. I take evolutionary psychology's understanding of manifest behavior as a point of departure, and then analyze the manifest behavior in terms of judgments, which are binary measurements at a particular point of reference; in other words, a given manifest behavior either did or did not occur at a particular point in time. I then show that judgments can 1) transmit from one individual to the next, 2) vary according to predictable adaptive processes, and 3) are either extinguished or flourish dependent upon the process of natural selection; judgments, therefore, meet the three requirements of evolutionary theory. Judgments, rather than genes, better describe the process of human political and social evolution, which becomes especially clear when one assesses the consequences of what I term "differential" outcomes in judgments.Item Genetic and biochemical dissection of complex evolved traits in bacteria(2014-08) Quandt, Erik Michael; Georgiou, George; Ellington, Andrew D.; Barrick, Jeffrey E; Alper, Hal S; Molineux, Ian JEvolutionary innovations often arise from complex genetic and ecological interactions, which can make it challenging to understand retrospectively how a novel trait arose. In a long-term experiment, Escherichia coli gained the ability (Cit⁺ ) to utilize abundant citrate in the growth medium after ~31,500 generations of evolution. Exploiting this previously untapped resource was highly beneficial: later Cit⁺ variants achieve a much higher population density in this environment. All Cit⁺ individuals share a mutation that activates aerobic expression of the citT citrate:C₄-dicarboxylate antiporter, but this mutation confers only an extremely weak Cit⁺ phenotype on its own. To determine which of the other >70 mutations in early Cit⁺ clones were needed to take full advantage of citrate, we developed a Recursive Genome-Wide Recombination and Sequencing (REGRES) method and performed genetic backcrosses to purge mutations not required for Cit⁺ from an evolved strain. We discovered a mutation that increased expression of the dctA C₄-dicarboxylate transporter greatly enhanced the Cit⁺ phenotype after it evolved, implicating the intracellular supply of succinate or other C₄-dicarboxylates to be a critical factor for the expression of the phenotype. The activity level of citrate synthase (CS), encoded by the gltA gene, was also found to be important for Cit⁺. A mutation to gltA (gltA1) occurred before the evolution of Cit⁺ and led to an increase in CS activity by diminishing allosteric inhibition by NADH. This mutation was found to be deleterious for high-level citrate utilization, a situation that was remedied shortly after the evolution of Cit⁺ by the evolution of compensatory mutations to gltA which decreased CS activity. We speculate that the gltA1 mutation may have been important to 'potentiate' the evolution of a weak Cit⁺ phenotype by increasing succinate production via an upregulated glyoxylate pathway but that as cells became able to import succinate by virtue of the dctA mutation that this pathway became maladaptive, prompting this evolutionary reversal. Overall, our characterization of this metabolic innovation highlights the degree to which interactions between alleles shape the evolution of complex traits and emphasizes the need for novel whole-genome methods to explore such relationships.
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